Yes, pedals. I'm pigeon toed and I think that was causing a lot of my pain. The frogs don't auto-center - if my feet want to stay in an off-center position (which they do) the Frogs are okay with that. After I switched the pain went away for a while. It's just recently come back.
Speedplay Frogs:
http://www.speedplay.com/index.cfm?fuseaction=home.frog
The Frogs aren't perfect for a few different reasons. I'm thinking about giving Bebops a try:
http://www.bebop.com/